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1 + \appendix
2   \chapter{\label{chapt:appendix}APPENDIX}
3  
4   Designing object-oriented software is hard, and designing reusable
5   object-oriented scientific software is even harder. Absence of
6   applying modern software development practices is the bottleneck of
7 < Scientific Computing community\cite{wilson}. For instance, in the
7 > Scientific Computing community\cite{Wilson}. For instance, in the
8   last 20 years , there are quite a few MD packages that were
9   developed to solve common MD problems and perform robust simulations
10   . However, many of the codes are legacy programs that are either
# Line 18 | Line 19 | in software design. Although originated as an architec
19  
20   Design patterns are optimal solutions to commonly-occurring problems
21   in software design. Although originated as an architectural concept
22 < for buildings and towns by Christopher Alexander \cite{alexander},
23 < software patterns first became popular with the wide acceptance of
24 < the book, Design Patterns: Elements of Reusable Object-Oriented
25 < Software \cite{gamma94}. Patterns reflect the experience, knowledge
26 < and insights of developers who have successfully used these patterns
27 < in their own work. Patterns are reusable. They provide a ready-made
28 < solution that can be adapted to different problems as necessary.
29 < Pattern are expressive. they provide a common vocabulary of
30 < solutions that can express large solutions succinctly.
22 > for buildings and towns by Christopher Alexander
23 > \cite{Alexander1987}, software patterns first became popular with
24 > the wide acceptance of the book, Design Patterns: Elements of
25 > Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect
26 > the experience, knowledge and insights of developers who have
27 > successfully used these patterns in their own work. Patterns are
28 > reusable. They provide a ready-made solution that can be adapted to
29 > different problems as necessary. Pattern are expressive. they
30 > provide a common vocabulary of solutions that can express large
31 > solutions succinctly.
32  
33   Patterns are usually described using a format that includes the
34   following information:
# Line 83 | Line 85 | freedom.  Here is a diagram of the class heirarchy:
85   collections of atoms or atoms which have orientational degrees of
86   freedom.  Here is a diagram of the class heirarchy:
87  
88 < \begin{figure}
89 < \centering
90 < \includegraphics[width=3in]{heirarchy.pdf}
91 < \caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
92 < The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
93 < selection syntax allows the user to select any of the objects that
94 < are descended from a StuntDouble.} \label{oopseFig:heirarchy}
95 < \end{figure}
88 > %\begin{figure}
89 > %\centering
90 > %\includegraphics[width=3in]{heirarchy.eps}
91 > %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
92 > %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
93 > %selection syntax allows the user to select any of the objects that
94 > %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
95 > %\end{figure}
96  
97   \begin{itemize}
98   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
# Line 143 | Line 145 | not & ``!''  \\
145   \subsection{\label{appendixSection:name}Name expressions}
146  
147   \begin{center}
148 < \begin{tabular}{|llp{3in}|}
148 > \begin{tabular}{|llp{2in}|}
149   \hline {\bf type of expression} & {\bf examples} & {\bf translation
150   of
151   examples} \\
# Line 227 | Line 229 | For example, the phrase {\tt select mass > 16.0 and ch
229   \end{center}
230  
231   For example, the phrase {\tt select mass > 16.0 and charge < -2}
232 < wouldselect StuntDoubles which have mass greater than 16.0 and
232 > would select StuntDoubles which have mass greater than 16.0 and
233   charges less than -2.
234  
235   \subsection{\label{appendixSection:within}Within expressions}
# Line 336 | Line 338 | distribution functions are most easily seen in the fig
338  
339   \begin{figure}
340   \centering
341 < \includegraphics[width=3in]{definition.pdf}
341 > \includegraphics[width=3in]{definition.eps}
342   \caption[Definitions of the angles between directional objects]{ \\
343   Any two directional objects (DirectionalAtoms and RigidBodies) have
344   a set of two angles ($\theta$, and $\omega$) between the z-axes of

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